Hem S. Bhandari

Characterization of the Rust Fungus, Puccinia emaculata, and Evaluation of Genetic Variability for Rust Resistance in Switchgrass Populations

Several fungal pathogens have been identified on ornamental and native stands of switchgrass (Panicum virgatum L.). Diseases of switchgrass, particularly rust, have been largely neglected and are likely to become the major limiting factor to biomass yield and quality, especially when monocultured over a large acreage. Based on teliospore morphology and internal transcribed spacer-based diagnostic primers, the rust pathogen collected from switchgrass research fields in Oklahoma was identified as Puccinia emaculata. Furthermore, to identify genetically diverse source(s) of rust resistance, several switchgrass genotypes from both upland (cv. ‘Summer’ and ‘Cave-in-Rock’) and lowland (cv. ‘Alamo’ and ‘Kanlow’) ecotypes were evaluated in Ardmore, Oklahoma during 2008 and 2009 and in growth chamber assays. Field and growth chamber evaluations revealed a high degree of genetic variation within and among switchgrass cultivars. In general, Alamo and Kanlow showed moderate resistance to P. emaculata, while Summer was highly susceptible. Distinct ecotypic variations for reactions to rust were also prevalent with the lowlands maintaining a high level of resistance. These results suggest the potential for improvement of rust resistance via the selection of resistant individuals from currently available cultivars. Further, the selection pressure on the pathogen would also be reduced by employing several rust resistant cultivars in production-scale situations.

Effects of ecotypes and morphotypes in feedstock composition of switchgrass (Panicum virgatum L.)

Switchgrass (Panicum virgatum L.) is a C4 grass with high biomass yield potential and is now a model species for the Bioenergy Feedstock Development Program. Two distinct ecotypes (e.g., upland and lowland) and a range of plant morphotypes (e.g., leafy and stemmy) have been observed in switchgrass. The objective of this study was to determine the influence of ecotype and morphotype on biomass feedstock quality. Leaf and stem tissues of leafy and stemmy morphotypes from both lowland and upland ecotypes were analyzed for key feedstock traits. The leaf : stem ratio of leafy morphotype was more than 40% higher than the stemmy morphotype in both upland and lowland ecotypes. Therefore, the stemmy morphotype has significant advantages over leafy morphotype during harvesting, storage, transportation and finally the feedstock quality. Remarkable differences in feedstock quality and mineral composition were observed in switchgrass genotypes with distinct ecotypic origins and variable plant morphotypes. Lignin, hemicelluloses and cellulose concentrations were higher in stems than in the leaves, while ash content was notably high in leaves. A higher concentration of potassium was found in the stems compared to the leaves. In contrast, calcium was higher and magnesium was generally higher in the leaves compared to stems. The upland genotypes demonstrated considerably higher lignin (14.4%) compared with lowland genotypes (12.4%), while hemicellulose was higher in lowland compared with upland. The stemmy type demonstrated slightly higher lignin compared with leafy types (P < 0.1). Differences between the ecotypes and morphotypes for key quality traits demonstrated the potential for improving feedstock composition of switchgrass through selection in breeding programs.

Genetic Variation in Lowland Switchgrass (Panicum virgatum L.)

Switchgrass (Panicum virgatum L.) is identified as one of the main cellulosic biofuel feedstocks in the USA. Understanding genetic variation for biomass yield in switchgrass would be helpful in determining the appropriate breeding approach for cultivar development. In order to estimate the genetic component of variation in lowland switchgrass, 10 half-sib families and 47 full-sib families produced by making crosses between selected genotypes from one of the Noble Foundation’s lowland breeding populations were evaluated in a nested design. The seedlings of these 47 families, and two checks, ‘Alamo’ and ‘Blade™ EG1101’, were established in the greenhouse and transplanted in late summer of 2007 at two Oklahoma (USA) locations, Ardmore and Burneyville, using a honeycomb planting design with 1.5 m plant-spacing. Each family was represented by 30 genotypes, including 15 reciprocals, at each location. The biomass from individual plants was harvested separately after the killing frost in 2008. Genetic components of variation were estimated following the mixed model in SAS, and heritability was estimated. Significant effects due to half-sib and full-sib families suggested both additive and non-additive gene actions were important in biomass dry matter yields of lowland switchgrass. The heritability estimates based on family analysis (0.33) and parent-progeny regression (0.18) were low, suggesting that the trait was under the control of many genes with minor effects and influenced by significant environmental effects. Developing high yielding switchgrass cultivars will probably need to exploit both additive and non-additive gene effects and selection and testing will need to be done in the target environments.

Switchgrass as a bioenergy feedstock: advances in breeding and genomics research

Switchgrass (Panicum virgatum L), a native perennial of the North American prairie, possesses high biomass yield potential in marginal environments with limited input. It is an outcrossing tetraploid (2n = 4x = 36) with disomic inheritance. Previous research on cultivar improvement was focused primarily on herbage yield and forage digestibility. The decision of the U.S. Department of Energy Biomass Feedstock Development Program (NFDP) to develop switchgrass as a lignocellulosic bioenergy feedstock in the USA in the 1990s prompted a growing motivation for breeding and genomics research. The species is in early stages of domestication and current cultivars include mostly early releases for forage use that were selected directly from collected strains. Recent releases specifically for biomass feedstock have undergone one or two cycles of selection. As an outcrossing self-incompatible species, switchgrass possesses ample genetic diversity both between and within native populations. Conventional population improvement approaches such as recurrent restricted phenotypic selection (RRPS) are effective in improving forage yield and digestibility. Hybrids between different populations also demonstrated heterosis for key feedstock traits. However, genetic gains per year from selection using conventional approaches are low due to perennial growth habit and low heritability of important traits. Genomic approaches could be helpful in improving selection gain. Significant efforts have been placed in developing genomics resources. Genetic linkage maps were published and a large number of DNA-based markers were developed. Whole-genome sequencing is near completion, and the genetic bases of inheritance of key feedstock traits are being investigated. New insights into the molecular mechanisms will enable tailoring more efficient cultivar breeding approaches in the future.

Identifying and exploring significant genomic regions associated with soybean yield, seed fatty acids, protein and oil

Soybean [Glycine max (L.) Merrill] yield and seed fatty acids, protein, and oil content are important traits for which an improved understanding of significant genomic regions would be useful. To accomplish this, a soybean population consisting of 203 F5 derived recombinant inbred lines (RILs) was developed and genotyped with 11,633 polymorphic single nucleotide polymorphisms (SNPs). Each RIL was grown in a single plot at Knoxville, TN in 2010; followed by replicated, multi-location field trials in 2013 and 2014. The data from 2010, 2013, and 2014 were analyzed together in order to detect quantitative trait loci (QTL) for these traits, and 30 total QTLs were detected. Five QTLs are candidates for confirmed status and one QTL is a candidate for positional confirmation. Many of the genes with mutations in close proximity to the fatty acid QTLs are involved in biological processes for fatty acids and/or lipids and could be considered possible candidate genes. Similarly, genes with mutations in genomic regions near yield, protein, and oil QTLs were plentiful and may contribute to the variation observed in these traits. Except for yield and stearic acid, each trait displayed pleiotropic effects with other traits in this study. Notable are the pleiotropic effects for oleic and linolenic acid on chromosomes 9, 13, and 19. Overall, the findings from this research contribute new information to the genetic understanding of soybean yield and seed fatty acids, protein and oil content. This understanding will be useful in making trait improvements.